Specifically, what makes a good villain in a Roleplay setting. How do you go about crafting a worthy antagonist for your players? What do you keep in mind while you're creating the big bad, and what differentiates a mediocre baddie from a quality villain?

How do RP antagonists differ from standard antagonists in other fiction, such as novels and film?

The above link gives many examples of bad villains, and does point out a small pool of traits that good villains should have.

First, I should note that antagonists and villains aren't the same thing, but they are usually interchangeable. an antagonist opposes the protagonist, who is the spotlight of the story. Where as a villain is someone who commits evil acts. An example of a story where the villain isn't an antagonist is death note. Light is most certainly the villain of the story, but he's the protagonist. This is important to consider, because what you really want is someone who is going to oppose the players in the story.

A good antagonist opposes the protagonists, which is usually going to be the bulk of the players in the RP. Anyone playing an antagonistic character should have a goal that puts them at odds with the other players. You could have a standard villain who just wants to kill everyone and everything, but he might not be more important than the players tasks, or the players might not find him worth dealing with because some of them are selfish in nature. Say the players are taking a purification crystal to the center of the largest ocean to purify the world's water supply. A crazy serial murderer/rapist/arson/mastermind isn't really a good obstacle for our characters. So what they plan on wiping out a city, if we don't get this crystal to the ocean, the whole world will die! Now, maybe our antagonist knows about this crystal, and wants to use it to resurrect a long dead civilization. The consequences of using the crystal this way is that it won't be able to purify the ocean, and 95% of the world will die of thirst or poison. Even the players with more selfish ambitions will be disappointed that they won't get paid for carrying out this mission. THAT antagonist is one that all of the players are going to be watching out for.